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In leaving a comment on the Vulcan nerve pinch question, it occurred to me that there was (Surprise surprise) a fairly big inconsistency regarding Khan and phaser fire.

When assaulting the bridge of the USS Vengeance, Khan is stunned and felled instantly. While the effects were short lived, he was stunned and out.

However, when participating in the aerial fight on the floating barge, Uhura stuns Khan several times with phaser fire. While it does stop him from moving forward, it does not produce unconsciousness.

Was there a difference in the phasers being used between the two scenes, or is this a plot inconsistency?

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There is no difference in the phasers, but in the situations. The one time Khan gets hit by surprise, the other time he sees the attack coming.

Long answer

When Kirk storms the bridge of the USS Vengeance together with Khan and Scotty, they take take out the whole crew except for the Commander. Kirk then gives Scotty a sign by nodding at him, after which Scotty fires a phaser burst at the unsuspecting Khan, taking him completely by surprise.

enter image description here Khan is out cold. Is he really, though?

That is exactly what Kirk and Scotty planned prior to the attack:

KIRK: The minute we get to the bridge, drop him.
SCOTTY: What? Stun him? Khan? I thought he was helping us!
KIRK: I am pretty sure we are helping him.

Khan is not prepared for this surprise attack from the people who he thought to be working with him.

I believe that is the main difference to the other incident you mention, the fight on the floating barge:

While Uhura teleports in behind Khan, he still becomes aware of her presence in time to turn around and engage her.

enter image description here

He sees her pointing the phaser at him and is able to physically and mentally prepare for the attack. This is enough for the genetically improved Khan to withstand multiple phaser shots without being knocked down. It still has a severe effect on him and allows Spock to finally overpower him.

(Screenshots and Transcript taken directly from the movie)

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How do you figure in the beating that he and Spock have been giving each other? Presumably that is much worse than anything he took from the limited number of personnel he engaged on the way to the bridge. – JohnP Jun 4 '14 at 16:35
I suspect that his powers are great enough that he would have been able to withstand the phasers much easier and take down Uhura if he wasn't already exhausted at this point. – atticae Jun 4 '14 at 16:36
The only in-universe explanation that makes sense to me is that he has to prepare himself to withstand the phaser shot. If you watch the barge scene, you see that he has a few seconds before Uhura shoots him. As I said above, he simply was not ready when Scotty hit him. – atticae Jun 4 '14 at 16:37
I just watched the scene (There's a clip on youtube), and Khan sees her, turns back to Spock to start to stand up, and the first shot hits him before he is looking at her. Second shot just as he stands and turns. – JohnP Jun 4 '14 at 16:53
Personally, I assumed Khan's reaction upon getting stunned on the bridge of the Vengence was a ruse - he was never actually stunned. I believe he acted stunned due to not having the tactical advantage. In that scene, there were at least two (Kirk/Scotty -- I don't remember if Carol Marcus had one) which had phasers on him or at the ready. If he took one out, the other could flip over from stun to kill in a matter of moments and take him out permanently. Acting stunned allowed him to gain the tactical advantage of surprise, which worked very well. – Pᴀᴜʟsᴛᴇʀ2 Jun 4 '14 at 17:55

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